Overview of MODMS, including the construction pipeline for multi-omics data integration.
Newswise — Dubbed the “king of forages,” alfalfa is indispensable in agriculture for its high protein content, environmental adaptability, and role across diverse climates. With growing demands for livestock feed and increased environmental stresses, improving alfalfa’s resilience, yield, and nutritional profile has become critical. Although traditional methods have revealed valuable insights, integrating data across multiple biological systems remains challenging. Addressing these challenges, multi-omics database of M. sativa (MODMS) offers a sophisticated solution for comprehensive alfalfa research, advancing both crop performance and resilience.
Developed by Lanzhou University and set for publication (DOI: 10.1093/hr/uhad245) on November 27, 2023, in Horticulture Research, MODMS represents a new chapter in functional genomics for alfalfa. This open-access database consolidates genetic, transcriptomic, proteomic, and metabolomic datasets, designed for an intuitive user experience. MODMS enables users to compare genome sequences and analyze complex gene functions, with applications extending from academic research to practical breeding. Accessible at https://modms.lzu.edu.cn/, MODMS is positioned to become a cornerstone in advancing alfalfa research worldwide.
MODMS facilitates comprehensive analysis of alfalfa through seven main modules: genomics, transcriptomics, gene variations, proteomics, metabolomics, guide RNA (gRNA) design, and bioinformatics tools. The platform's features include genome alignment, sequence retrieval, and visual data comparisons. Highlights include the genomic module, which enables gene structure and genome collinearity analysis, along with variation analysis across multiple alfalfa varieties. The transcriptomic module offers insights into gene expression under various conditions, while proteomics and metabolomics modules support detailed analysis of protein interactions and metabolic responses. Furthermore, MODMS's gRNA tool enables precision gene-editing by allowing researchers to develop customized gRNAs for specific gene sequences, supporting gene editing for traits such as stress tolerance and enhanced adaptability. By integrating data across biological levels, MODMS stands to reshape research on key agronomic traits, promoting strides in breeding and crop resilience.
Dr. Zhipeng Liu, lead researcher at Lanzhou University’s State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, underscores MODMS's significance: “MODMS opens unparalleled avenues for alfalfa research by unifying multi-omics data into a single, cohesive platform. As agricultural demands increase, researchers require tools that support in-depth genetic and agronomic analysis. MODMS delivers a comprehensive resource that fosters productivity and adaptability improvements in alfalfa, critical for sustainable agriculture.”
Beyond research, MODMS supports breeders and agriculturalists in developing climate-resilient and nutrient-rich alfalfa varieties. By revealing genetic pathways associated with stress tolerance and agronomic traits, the database aids in pinpointing key genes for targeted breeding. Additionally, the platform's genomic and proteomic tools are expected to benefit research on other crops, positioning MODMS as a vital resource in forage crop bioinformatics. Future expansion with more datasets and refined analysis tools will likely broaden MODMS’s scope and utility even further.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhad245
Funding information
This work was partly supported by the National Key Research and Development Program (2022YFF1003200), and the National Natural Science Foundation of China (Grant No. 32201463 and 32201444). We received support from the Supercomputing Center of Lanzhou University.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.
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